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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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Prodial .gbk output has no sequences in it. #71

Open Rob-murphys opened 4 years ago

Rob-murphys commented 4 years ago

I am running prodigal of a hybrid assembled genome using the following command:

prodigal -i $assembly -o $path/annotated/$outdir -a $path/annotated/$protein

and I get the following logs:


-------------------------------------
PRODIGAL v2.6.3 [February, 2016]
Univ of Tenn / Oak Ridge National Lab
Doug Hyatt, Loren Hauser, et al.
-------------------------------------
Request:  Single Genome, Phase:  Training
Reading in the sequence(s) to train...8636137 bp seq created, 71.60 pct GC
Locating all potential starts and stops...468410 nodes
Looking for GC bias in different frames...frame bias scores: 0.75 0.12 2.13
Building initial set of genes to train from...done!
Creating coding model and scoring nodes...done!
Examining upstream regions and training starts...done!
-------------------------------------
Request:  Single Genome, Phase:  Gene Finding
Finding genes in sequence #1 (6367 bp)...done!
Finding genes in sequence #2 (335340 bp)...done!
Finding genes in sequence #3 (73807 bp)...done!
Finding genes in sequence #4 (244411 bp)...done!
Finding genes in sequence #5 (662766 bp)...done!
Finding genes in sequence #6 (85141 bp)...done!
Finding genes in sequence #7 (33726 bp)...done!
Finding genes in sequence #8 (216105 bp)...done!
Finding genes in sequence #9 (178762 bp)...done!
Finding genes in sequence #10 (156481 bp)...done!
Finding genes in sequence #11 (3611 bp)...done!
Finding genes in sequence #12 (2911 bp)...done!
Finding genes in sequence #13 (182115 bp)...done!
Finding genes in sequence #14 (132779 bp)...done!
Finding genes in sequence #15 (67154 bp)...done!
Finding genes in sequence #16 (281689 bp)...done!
Finding genes in sequence #17 (3062 bp)...done!
Finding genes in sequence #18 (3305 bp)...done!
Finding genes in sequence #19 (4174 bp)...done!
Finding genes in sequence #20 (79222 bp)...done!
Finding genes in sequence #21 (169958 bp)...done!
Finding genes in sequence #22 (86629 bp)...done!
Finding genes in sequence #23 (2666 bp)...done!
Finding genes in sequence #24 (80935 bp)...done!
Finding genes in sequence #25 (91451 bp)...done!
Finding genes in sequence #26 (6694 bp)...done!
Finding genes in sequence #27 (129948 bp)...done!
Finding genes in sequence #28 (39582 bp)...done!
Finding genes in sequence #29 (4005 bp)...done!
Finding genes in sequence #30 (154412 bp)...done!
Finding genes in sequence #31 (3093 bp)...done!
Finding genes in sequence #32 (2867 bp)...done!
Finding genes in sequence #33 (3281 bp)...done!
Finding genes in sequence #34 (3072 bp)...done!
Finding genes in sequence #35 (3960 bp)...done!
Finding genes in sequence #36 (2801 bp)...done!
Finding genes in sequence #37 (4075 bp)...done!
Finding genes in sequence #38 (4093 bp)...done!
Finding genes in sequence #39 (6544 bp)...done!
Finding genes in sequence #40 (6646 bp)...done!
Finding genes in sequence #41 (166538 bp)...done!
Finding genes in sequence #42 (3788 bp)...done!
Finding genes in sequence #43 (4055 bp)...done!
Finding genes in sequence #44 (6488 bp)...done!
Finding genes in sequence #45 (3391 bp)...done!
Finding genes in sequence #46 (2872 bp)...done!
Finding genes in sequence #47 (2900 bp)...done!
Finding genes in sequence #48 (3021 bp)...done!
Finding genes in sequence #49 (3057 bp)...done!
Finding genes in sequence #50 (2920 bp)...done!
Finding genes in sequence #51 (3551 bp)...done!
Finding genes in sequence #52 (4162 bp)...done!
Finding genes in sequence #53 (5764 bp)...done!
Finding genes in sequence #54 (2898 bp)...done!
Finding genes in sequence #55 (6889 bp)...done!
Finding genes in sequence #56 (6656 bp)...done!
Finding genes in sequence #57 (1890102 bp)...done!
Finding genes in sequence #58 (5322 bp)...done!
Finding genes in sequence #59 (559988 bp)...done!
Finding genes in sequence #60 (198038 bp)...done!
Finding genes in sequence #61 (3615 bp)...done!
Finding genes in sequence #62 (3362 bp)...done!
Finding genes in sequence #63 (1724353 bp)...done!
Finding genes in sequence #64 (6227 bp)...done!
Finding genes in sequence #65 (9556 bp)...done!
Finding genes in sequence #66 (8497 bp)...done!
Finding genes in sequence #67 (52808 bp)...done!
Finding genes in sequence #68 (4817 bp)...done!
Finding genes in sequence #69 (2927 bp)...done!
Finding genes in sequence #70 (2733 bp)...done!
Finding genes in sequence #71 (3396 bp)...done!
Finding genes in sequence #72 (71739 bp)...done!
Finding genes in sequence #73 (5682 bp)...done!
Finding genes in sequence #74 (2841 bp)...done!
Finding genes in sequence #75 (94252 bp)...done!
Finding genes in sequence #76 (8082 bp)...done!
Finding genes in sequence #77 (3267 bp)...done!
Finding genes in sequence #78 (5193 bp)...done!
Finding genes in sequence #79 (62172 bp)...done!
Finding genes in sequence #80 (4135 bp)...done!
Finding genes in sequence #81 (3907 bp)...done!
Finding genes in sequence #82 (23435 bp)...done!
Finding genes in sequence #83 (4499 bp)...done!
Finding genes in sequence #84 (3955 bp)...done!
Finding genes in sequence #85 (4094 bp)...done!
Finding genes in sequence #86 (4104 bp)...done!
Finding genes in sequence #87 (7306 bp)...done!
Finding genes in sequence #88 (7334 bp)...done!
Finding genes in sequence #89 (30240 bp)...done!
Finding genes in sequence #90 (24489 bp)...done!

However when attempting to open the .gbk output in Artemis I get an error saying no sequences found in the file and upon ispecting the file I see the following:


DEFINITION  seqnum=1;seqlen=6367;seqhdr="tig00000005_pilon";version=Prodigal.v2.6.3;run_type=Single;model="Ab initio";gc_cont=71.60;transl_table=11;uses_sd=1
FEATURES             Location/Qualifiers
     CDS             complement(<3..1202)
                     /note="ID=1_1;partial=10;start_type=ATG;rbs_motif=AGGAG;rbs_spacer=5-10bp;gc_cont=0.728;conf=99.99;score=272.46;cscore=254.78;sscore=17.67;rscore=12.98;uscore=0.26;tscore=5.09;"
     CDS             complement(1391..2011)
                     /note="ID=1_2;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.728;conf=100.00;score=101.95;cscore=100.13;sscore=1.82;rscore=-4.68;uscore=0.51;tscore=5.09;"
     CDS             complement(2046..2909)
                     /note="ID=1_3;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.721;conf=100.00;score=160.96;cscore=151.32;sscore=9.64;rscore=0.90;uscore=2.35;tscore=5.09;"
     CDS             complement(2906..3178)
                     /note="ID=1_4;partial=00;start_type=GTG;rbs_motif=3Base/5BMM;rbs_spacer=13-15bp;gc_cont=0.711;conf=99.16;score=20.75;cscore=26.91;sscore=-6.15;rscore=-3.37;uscore=0.41;tscore=-2.53;"
     CDS             3203..3475
                     /note="ID=1_5;partial=00;start_type=GTG;rbs_motif=GGA/GAG/AGG;rbs_spacer=11-12bp;gc_cont=0.707;conf=99.34;score=21.79;cscore=26.91;sscore=-5.11;rscore=-2.13;uscore=-0.45;tscore=-2.53;"
     CDS             3472..4989
                     /note="ID=1_6;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.727;conf=99.99;score=230.88;cscore=221.25;sscore=9.64;rscore=0.90;uscore=2.35;tscore=5.09;"
     CDS             5331..6161
                     /note="ID=1_7;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.708;conf=100.00;score=90.98;cscore=99.88;sscore=-8.90;rscore=-4.68;uscore=-1.03;tscore=-2.53;"
     CDS             6140..>6367
                     /note="ID=1_8;partial=01;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.750;conf=96.70;score=14.70;cscore=17.46;sscore=-2.76;rscore=-4.68;uscore=-3.17;tscore=5.09;"
//

Any idea what is happening?

tseemann commented 4 years ago

I think Prodigal does not generate a "full" genbank record, only the annotation part.

For Artemis I think you can open it like this:

art  $assembly + prodigal.gbk

The contigs, then a +, then the annotations